8JZG | pdb_00008jzg

C. glutamicum S-adenosylmethionine synthase co-crystallized with Adenosine, triphosphate, and SAM

PDB DOI: https://doi.org/10.2210/pdb8JZG/pdb

Classification: TRANSFERASE
Organism(s): Corynebacterium glutamicum ATCC 13032
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-07-05 Released: 2023-10-25
Deposition Author(s): Lee, S., Kim, K.J.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.39 Å
R-Value Free:
0.260 (Depositor), 0.268 (DCC)
R-Value Work:
0.194 (Depositor), 0.198 (DCC)
R-Value Observed:
0.198 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structural and Biochemical Studies on Product Inhibition of S-Adenosylmethionine Synthetase from Corynebacterium glutamicum .

Lee, S., Kim, S., Kim, I.K., Kim, K.J.

(2023) J Agric Food Chem 71: 15692-15700

PubMed: 37846083 Search on PubMed
DOI: https://doi.org/10.1021/acs.jafc.3c05180
Primary Citation Related Structures:
8JZG, 8JZH, 8JZI

PubMed Abstract:
S-Adenosylmethionine (SAM) acts as a methyl donor in living organisms, and S-adenosylmethionine synthetase (MetK) is an essential enzyme for cells, as it synthesizes SAM from methionine and adenosine triphosphate (ATP). This study determined the crystal structures of the apo form and adenosine/triphosphate complex form of MetK from Corynebacterium glutamicum ( Cg MetK). Results showed that Cg MetK has an allosteric inhibitor binding site for the SAM product in the vicinity of the active site and is inhibited by SAM both competitively and noncompetitively. Through structure-guided protein engineering, the Cg MetK ^E68A variant was developed that exhibited an almost complete release of inhibition by SAM with rather enhanced enzyme activity. The crystal structure of the Cg MetK ^E68A variant revealed that the formation of a new hydrogen bond between Tyr66 and Glu102 by the E68A mutation disrupted the allosteric SAM binding site and also improved the protein thermal stability by strengthening the tetramerization of the enzyme.

Organizational Affiliation

School of Life Sciences, BK21 FOUR KNU Creative BioResearch Group, Kyungpook National University, Daegu 41566, Republic of Korea.

Macromolecule Content

Total Structure Weight: 181.31 kDa
Atom Count: 12,405
Modeled Residue Count: 1,548
Deposited Residue Count: 1,628
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
S-adenosylmethionine synthase	A, B, C, D	407	Corynebacterium glutamicum ATCC 13032	Mutation(s): 0 Gene Names: metK, Cgl1603, cg1806 EC: 2.5.1.6
UniProt
Find proteins for Q9K5E4 (Corynebacterium glutamicum (strain ATCC 13032 / DSM 20300 / JCM 1318 / BCRC 11384 / CCUG 27702 / LMG 3730 / NBRC 12168 / NCIMB 10025 / NRRL B-2784 / 534)) Explore Q9K5E4 Go to UniProtKB: Q9K5E4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9K5E4
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM (Subject of Investigation/LOI) Query on SAM Download:Ideal Coordinates CCD File SDF format, chain V [auth C] SDF format, chain P [auth B] SDF format, chain G [auth A] SDF format, chain BA [auth D] MOL2 format, chain V [auth C] MOL2 format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain BA [auth D] mmCIF format, chain V [auth C] mmCIF format, chain P [auth B] mmCIF format, chain G [auth A] mmCIF format, chain BA [auth D]	BA [auth D], G [auth A], P [auth B], V [auth C]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain BA [auth D] Focus chain G [auth A] Focus chain P [auth B] Focus chain V [auth C] Interactions & Density Focus chain BA [auth D] Focus chain G [auth A] Focus chain P [auth B] Focus chain V [auth C]
ADN (Subject of Investigation/LOI) Query on ADN Download:Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain T [auth C] SDF format, chain N [auth B] SDF format, chain E [auth A] MOL2 format, chain Z [auth D] MOL2 format, chain T [auth C] MOL2 format, chain N [auth B] MOL2 format, chain E [auth A] mmCIF format, chain Z [auth D] mmCIF format, chain T [auth C] mmCIF format, chain N [auth B] mmCIF format, chain E [auth A]	E [auth A], N [auth B], T [auth C], Z [auth D]	ADENOSINE C₁₀ H₁₃ N₅ O₄ OIRDTQYFTABQOQ-KQYNXXCUSA-N		Interactions Focus chain E [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain Z [auth D] Interactions & Density Focus chain E [auth A] Focus chain N [auth B] Focus chain T [auth C] Focus chain Z [auth D]
3PO (Subject of Investigation/LOI) Query on 3PO Download:Ideal Coordinates CCD File SDF format, chain U [auth C] SDF format, chain O [auth B] SDF format, chain F [auth A] SDF format, chain AA [auth D] MOL2 format, chain U [auth C] MOL2 format, chain O [auth B] MOL2 format, chain F [auth A] MOL2 format, chain AA [auth D] mmCIF format, chain U [auth C] mmCIF format, chain O [auth B] mmCIF format, chain F [auth A] mmCIF format, chain AA [auth D]	AA [auth D], F [auth A], O [auth B], U [auth C]	TRIPHOSPHATE H₅ O₁₀ P₃ UNXRWKVEANCORM-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain F [auth A] Focus chain O [auth B] Focus chain U [auth C] Interactions & Density Focus chain AA [auth D] Focus chain F [auth A] Focus chain O [auth B] Focus chain U [auth C]
POP (Subject of Investigation/LOI) Query on POP Download:Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	PYROPHOSPHATE 2- H₂ O₇ P₂ XPPKVPWEQAFLFU-UHFFFAOYSA-L		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain H [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain H [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain H [auth A]	H [auth A], Q [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain Q [auth B] Interactions & Density Focus chain H [auth A] Focus chain Q [auth B]
K (Subject of Investigation/LOI) Query on K Download:Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain EA [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain EA [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain EA [auth D]	EA [auth D], L [auth A], M [auth A], Y [auth C]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain EA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain Y [auth C] Interactions & Density Focus chain EA [auth D] Focus chain L [auth A] Focus chain M [auth A] Focus chain Y [auth C]
MG (Subject of Investigation/LOI) Query on MG Download:Ideal Coordinates CCD File SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain S [auth B] SDF format, chain R [auth B] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain DA [auth D] SDF format, chain CA [auth D] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain S [auth B] MOL2 format, chain R [auth B] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain DA [auth D] MOL2 format, chain CA [auth D] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain S [auth B] mmCIF format, chain R [auth B] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain DA [auth D] mmCIF format, chain CA [auth D]	CA [auth D] DA [auth D] J [auth A] K [auth A] R [auth B] CA [auth D], DA [auth D], J [auth A], K [auth A], R [auth B], S [auth B], W [auth C], X [auth C]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain CA [auth D] Focus chain DA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain CA [auth D] Focus chain DA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B] Focus chain W [auth C] Focus chain X [auth C]